Mounting the home partition at /home in the installer should work. Deleting the /home of the user you're logged in as isn't going to work because the applications you use to do it will most likely try to write something into ~/.local or .config, so it's never really empty. You could log into the root user though and do it from there.
Btw. It's not really beneficial to put your home partition on an HDD for the same reason. All Programs you use are going to have to access some hidden config or data files so it's going to slow everything down. (Also in case you use Steam, it installs all the games in ~/.local) A better way is to mount the HDD somewhere else and symlink your ~/Documents, ~/Pictures etc to the HDD.